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Vaughn Cooper

@vscooper.micropopbio.org
8K followers 1.6K following 1.7K posts

Evangelist for the study of evolution in action by everyone. Pitt Prof | ASM President|EvolvingSTEM | biofilms | EvMed | genomics entrepreneur (@SeqCoast.bsky.social, @midauthorbio.bsky.social)| exercise addict ~ swim bike run

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Reposted by Vaughn Cooper
Vivek Mutalik @vivekmutalik.bsky.social · 9h
In our brand new 🥳 review, @hemaa-selvakumar.bsky.social & team pull a scattered literature in phage biology into a coherent framework for scaling up to engineering complex communities. We poured our hearts into this to share challenges & future opportunities for the nextGen!
Next generation application space with systematic characterization of phage-host interaction landscapes.
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Josh Marshall @joshtpm.bsky.social · 9h
Best Sen Schmitt meme yet
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Carl Zimmer @carlzimmer.com · 28/09/2026
The human genome is part virus. And here's a virus that's part human, having picked up a human gene about 100,000 years ago. My story here: nyti.ms/4hRKNPC
nyti.ms
This Virus Stole a Human Gene and Won’t Let Go of It (Gift Article)
Scientists have found a human gene lurking in a virus that causes skin infections. It may be using our own DNA to infect us.
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Vaughn Cooper @vscooper.micropopbio.org · 27/09/2026
How do Burkholderia multivorans bacteria adaptively evolve during infections of the cystic fibrosis airway? A longtime collab and intensive study of 8 patients links bacterial adaptations to disease progression. Our findings also unite prior studies. www.biorxiv.org/content/10.6...
biorxiv.org
Convergent genetic evolution within Burkholderia multivorans chronic infections correlates with lung function decline in cystic fibrosis patients
The patterns and pathways of pathogen adaptation during chronic infections can reveal the gateways microbes must unlock to colonize and persist. In chronic lung infections of cystic fibrosis (CF) pati...
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The Ferrari Lab @theferrarilab.bsky.social · 27/09/2026
TT Assistant Professor position in Ecology and Evolution of Infectious Disease at University of Florida
explore.jobs.ufl.edu
University of Florida - Details - Assistant Professor of Biology
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C. Brandon Ogbunu @cbo.bsky.social · 27/09/2026
In my latest for @undark.org, I compare AI adoption in science to the Ship of Theseus: "If you swap out every wooden plank on a ship over time, is it still the same vessel?" I argue that science derives authority from something more than data generation + publication. undark.org/2026/09/25/o...
undark.org
AI Presents Science with a ‘Ship of Theseus’ Problem
Opinion | AI can replace each part of the scientific process, leaving the enterprise recognizable but devoid of human judgment.
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Kathleen Bachynski @bachynski.bsky.social · 27/09/2026
“Studying Paulinella, scientists hope, will elucidate one of the most fundamental transitions in the history of life on our planet — and possibly give clues to how it might happen elsewhere in the universe. It could also provide practical insights on how to engineer photosynthetic organisms”
nytimes.com
In an $80 Motel Room, a Discovery to Shed Light on the Origins of Life
A scrappy science project led to a significant discovery: two new species of a rare organism that could elucidate a fundamental transition in the history of life on our planet.
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Eric Topol @erictopol.bsky.social · 27/09/2026
The word of the day: Zombified www.nytimes.com/2026/09/26/h...
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Craig Kaplan @triggerloop.bsky.social · 25/09/2026
It is the case. The Biosketch has a certification so that happens when you generate the document. They updated the current certification to expire Sept 26. So you need new one
Action needed — Regenerate SciENcv documents before upcoming NIH and other federal submissions

The Office of Sponsored Programs (OSP) has become aware of time-sensitive issues affecting SciENcv generated documents.

SciENcv updated the digital certificate used to sign Biosketch and Current & Pending (Other) Support (CPOS) documents without notification. The old certificate expires Saturday, September 26, 2026. Documents downloaded from SciENcv before that date may fail validation in eRA Commons and generate errors that delay or block submission.

This certificate change affects applications and RPPRs to NIH, AHRQ, CDC, NIOSH, FDA, and VA submitted on or after September 26, whether they are submitted in PERIS™ MyFunding/System-to-System, ASSIST, or Grants.gov Workspace. Because SciENcv is also used to prepare Biosketch and CPOS documents for NSF, DOE, NASA, and USDA proposals, investigators with imminent submissions to those agencies are encouraged to regenerate their documents as a precaution.

What to do

Investigators should log back into SciENcv and regenerate their Biosketch and CPOS documents. When 'Download PDF' is selected, SciENcv will prompt the investigator to certify. The new PDFs should replace any older versions in in-progress applications.

October 5 R01 deadline

Any in-progress application that already includes Biosketch or CPOS documents will need those documents regenerated and replaced this coming week.
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Vaughn Cooper @vscooper.micropopbio.org · 25/09/2026
FYI to everyone submitting this October NIH cycle You need to re-certify your ScienCV AFTER Sept 26 (tomorrow) for your application or it may not be accepted. Great timing!
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PLOS Biology @plosbiology.org · 25/09/2026
#PhageTherapy can fail when the immune system makes antibodies against therapeutic viruses. This study shows that fiber- and nozzle-specific antibodies block phage infection and promote aggregation-driven, Fc receptor-independent phagocytosis. 🧪 #ImmuneSky #structure #virus buff.ly/J0FOg9g
The image shows a reconstructed model of antibody-induced phage aggregation. Phage therapy, which uses bacteria-specific viruses to treat bacterial infections, is a highly promising therapeutic strategy in the era of precision medicine. Increasing evidence suggests that antibodies generated during phage therapy can affect the efficacy of phage therapy and, in some cases, even lead to treatment failure. However, the molecular mechanisms by which phage-specific antibodies cause phage therapy failure remain to be elucidated. Using Acinetobacter baumannii and its podovirus phage AbP20 as a model, the authors revealed the antibodies targeting phage fiber and nozzle proteins induced the formation of large-sized tail-to-tail phage aggregates which possess reduced infection and facilitated susceptibility to phagocytosis, providing a new clue to understand phage-specific antibodies induced therapy failure.  
This image was created by Heng Xue and Hang Yang.
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Kate Baker @ksbakes.bsky.social · 25/09/2026
We have an open Assistant/Associate Professor position in Pathogen Biology at the Department of Genetics - come and join us! 🦠 🧫 🧬https://www.cam.ac.uk/jobs/assistantassociate-professor-in-pathogen-genetics-pc51175
cam.ac.uk
Assistant/Associate Professor in Pathogen Genetics
Applications are invited for an Assistant or Associate Professorship in Pathogen Genetics to be held in the Department of Genetics. We are searching for a talented individual with a track record of fu...
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NPR @npr.org · 24/09/2026
Stories of science funding being cut, labs shutting down and scientists losing jobs have flooded the media under Trump's administration. These six graphics show how those changes have affected U.S. biomedical research. n.pr/4ycseLJ
n.pr
Under Trump, NIH funding disruptions have evolved. Here's what the numbers show
Stories of science funding being cut, labs shutting down and scientists losing jobs have flooded the media under Trump's administration. These six graphics show how those changes have affected U.S. biomedical research.
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Joshua Weitz @joshuasweitz.bsky.social · 25/09/2026
FAI provides a window into a conservative re-imagining of science, one that might sound like it is focused on flourishing, but starts with vitriol and animus towards the very people who have driven US science forward and whose goal is the politicization of research (with a preferred winner).
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Joshua Weitz @joshuasweitz.bsky.social · 25/09/2026
He is not alone. Amidst 1.5+ years of attacks on science, there is well-funded, ascendant support for justifying the dismantling of America's leading scientific institutions from groups who will tell you, unmoored from evidence, that NIH, NSF, etc. were so flawed, that there was only one option.
FAI supporters

Our major philanthropic supporters have included Arnold Ventures, the Arthur N. Rupe Foundation, the Beth and Ravenel Curry Foundation, Coefficient Giving, the David and Lucile Packard Foundation, the Diana Davis Spencer Foundation, DonorsTrust, the Doris Duke Foundation, the Ethereum Foundation, the Filecoin Foundation for the Decentralized Web, the John S. and James L. Knight Foundation, the John Templeton Foundation, the Lynde and Harry Bradley Foundation, the Miles Foundation, the Proton Foundation, Recoding America Fund, Renaissance Philanthropy, the Sarah Scaife Foundation, the Searle Freedom Trust, the Silicon Valley Community Foundation, Stand Together Trust, Survival and Flourishing Fund, the Walton Family Foundation, the William and Flora Hewlett Foundation, and many others. Our corporate supporters and event sponsors have included a16z, Alphabet, Amazon, Anthropic, Astro Mechanica, Boom Supersonic, Cognition AI, DuckDuckGo, ExxonMobil, First Solar, Hadrian, Lightspeed Venture Partners, Meta, Microsoft, Mozilla, Narya Capital, New American Industrial Alliance, NRG Energy, Oklo, OpenAI, Paradigm Capital, Playground Global, Qualcomm, Rainmaker, Reflection AI, Shopify, Southern Company, T-Mobile, Uber, Ulysses, Variance, Waymo, XYZ Venture Capital, YCombinator, Yelp, Zanskar Geothermal, and various others. We are also grateful to our generous individual supporters who have chosen to remain anonymous.
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Erin Hotchkiss @fluvialbenthos.bsky.social · 24/09/2026
We (Biological Sciences at Virginia Tech) are #hiring TWO tenure-track Molecular Microbiology professors! Review of applications starts 1 Nov. I'm happy to answer questions about the department, VT, life in Blacksburg, etc.! More info / to apply: jobs.apply.vt.edu/jobs/assista... 🧪👩‍🔬🦠 #academicjobs
jobs.apply.vt.edu
Assistant/Associate Professor - Blacksburg, Virginia, United States
Job Description The Department of Biological Sciences in the College of Science at Virginia Tech seeks applicants for two (2) tenure-track research and teaching positions at the Assistant/Associate ...
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Craig Kaplan @triggerloop.bsky.social · 25/09/2026
This is so awesome
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Vaughn Cooper @vscooper.micropopbio.org · 23/09/2026
<shots fired> Why are consensus reviews authored by field leaders published in for-profit journals, instead of those run by the societies that serve those fields (and may have sponsored the workshop)? Disclosure: I’m a middle author of at least one, and it burns me.
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Vaughn Cooper @vscooper.micropopbio.org · 23/09/2026
Fantastic, comprehensive, useful review if you care about RNA modifications in bacteria: @asm.org @csdetweiler.bsky.social journals.asm.org/doi/10.1128/...
journals.asm.org
Compendium of RNA modifications for bacterial stress adaptation | Microbiology and Molecular Biology Reviews
SUMMARYRNA modifications in the tRNA, rRNA, and mRNA constitute a widespread layer of post-transcriptional gene regulation, commonly known as the epitranscriptome. In bacteria, tRNA and rRNA modificat...
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Harmit Singh Malik @harmitmalik.bsky.social · 21/09/2026
Thanks to the generosity of the Bezos Family Foundation, @basicsci.fredhutch.org is excited to announce a new search to recruit a Bezos Family Distinguished Scholar : apply.interfolio.com/193655
apply.interfolio.com
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
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tracey depellegrin @traceydepellegrin.bsky.social · 21/09/2026
The @c4lifesciences.bsky.social is seeking an Executive Director. CLS is a terrific group of engaged scientific & scholarly society leaders. Check out the position (ideal for a person experienced in policy & advocacy + Capitol Hill) & share w/interested, qualified folks.
ascb.applytojob.com
Executive Director, Coalition for the Life Sciences - American Society for Cell Biology (ASCB) - Career Page
Apply to Executive Director, Coalition for the Life Sciences at American Society for Cell Biology (ASCB) in Bethesda, MD.
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Mozammel Hoque @mozammel.bsky.social · 20/09/2026
1/ New paper out in ISME Communications now in full version. Bacteria rarely live alone in nature, so we ran a 6-month evolution experiment asking what happens when species are forced to share the same biofilm. Turns out, company changes everything. 🧵 doi.org/10.1093/isme...
doi.org
Mixed-species interactions constrain diversification and shape biofilm evolution
Abstract. Experimental evolution provides a powerful framework for dissecting how ecological interactions shape adaptive trajectories. Here, we evolved Kle
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Mozammel Hoque @mozammel.bsky.social · 20/09/2026
5/ Personal note, this is my first paper as last author, from my time at AIMI, UTS. Great collaboration with @vscooper.micropopbio.org, and huge thanks to my supervisors Diane McDougald and Scott Rice for their mentorship. This work was supported by the ARC. @arc-gov-au.bsky.social
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Vaughn Cooper @vscooper.micropopbio.org · 20/09/2026
Now published from a fun collaboration, please see 🧵 academic.oup.com/ismecommun/a...
academic.oup.com
Mixed-species interactions constrain diversification and shape biofilm evolution
Abstract. Experimental evolution provides a powerful framework for dissecting how ecological interactions shape adaptive trajectories. Here, we evolved Kle
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Ákos T Kovács @evolvedbiofilm.bsky.social · 19/09/2026
Mixed-species interactions constrain diversification and shape biofilm evolution Klebsiella pneumoniae + Pseudomonas protegens + Pseudomonas aeruginosa in ISME Communications from Mozammel Hoque, with Diane McDougald, Scott Rice, @vscooper.micropopbio.org academic.oup.com/ismecommun/a...
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Carl Zimmer @carlzimmer.com · 17/09/2026
I wrote about what came before CRISPR 4 billion years ago: a war among viruses. Gift link: nyti.ms/3TBq4q0
nyti.ms
The Next Gene-Editing Technology May Also Be the Oldest (Gift Article)
Scientists have discovered a powerful gene-targeting system in viruses. Billions of years old, VIPR seems to predate CRISPR and may be even more powerful.
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Carl Zimmer @carlzimmer.com · 17/09/2026
Pennsylvania measles outbreak now up to 731 cases and 4 deaths www.pa.gov/agencies/hea...
pa.gov
Measles
Measles is a disease that spreads easily from person to person and can make you sick. People who are not vaccinated are at the highest risk. The best protection against measles is vaccination. DOH is ...
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David Ho @davidho.bsky.social · 15/09/2026
NSF has reduced the research budget for all atmospheric, ocean, and earth sciences by ~80%. 80%! A lot of us will not be conducting new research or training new students for the foreseeable future.
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Vaughn Cooper @vscooper.micropopbio.org · 21/12/2023
Friends don't let friends publish in MDPI journals. Pass it on. For more info, check out the Wikipedia page: en.wikipedia.org/wiki/MDPI 🔥
en.wikipedia.org
MDPI - Wikipedia
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Asher Leeks @asherleeks.bsky.social · 16/09/2026
Come work with @viromehunter.bsky.social and myself at UBC! We have a postdoctoral position available for someone with an interest in bioinformatics and genomics, using sociovirology to understand disease dynamics in plant viruses. Advert: ppvlab.sites.olt.ubc.ca/files/2026/0...
ppvlab.sites.olt.ubc.ca
Browser Verification | UBC Cybersecurity
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Nature Microbiology @natmicrobiol.nature.com · 16/09/2026
Out Now! Prophage-encoding engineered bacteria enable prophylactic lytic phage therapy for enteric infection in mice #MicroSky
go.nature.com
Prophage-encoding engineered bacteria enable prophylactic lytic phage therapy for enteric infection in mice
Nature Microbiology, Published online: 16 September 2026; doi:10.1038/s41564-026-02484-3An engineered non-pathogenic bacterium produces lytic phages and is protective in mouse models of Salmonella infection.
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Vaughn Cooper @vscooper.micropopbio.org · 16/09/2026
Authors!🚨 While you scramble for scarce $ 🤔 “Springer Nature reports revenue growth of 6.2%..and adjusted operating profit growth of 7.7%. They reported even more stunning submission growth of 30% and published article growth of 13%.” Publishing in society journals helps YOU not them👇🏻. Pass it on.
static.klipy.com
Man Lying on a Pile of Money
ALT: Man Lying on a Pile of Money
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Hiten Madhani @hitenmadhani.bsky.social · 16/09/2026
Spot on piece about the relationship between Federally funded science and the development of therapies. Investors want ‘de-risked’ assets. It’s their favorite word.
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Will Ratcliff @wcratcliff.bsky.social · 15/09/2026
1/17 Submissions are now open for the 2027 Microbial Population Biology GRC! We expect this meeting to be extraordinarily oversubscribed. If you want to come, time is of the essence--apply ASAP! June 27–July 2 • Andover, NH www.grc.org/microbial-po...
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Vaughn Cooper @vscooper.micropopbio.org · 12/09/2026
Gotta love Sepp! www.nytimes.com/athletic/758...
nytimes.com
America’s Sepp Kuss is about to complete one of endurance sport’s hardest feats (again) (Gift Article)
Kuss is just days away from completing the Giro d'Italia, Tour de France and Vuelta a España in the same season, for a second time
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Diversify Microbiology @diversifymicro.bsky.social · 11/09/2026
UNC Greensboro Department of Biology is hiring for three positions this year including one in microbiology! spartantalent.uncg.edu/postings/35918
spartantalent.uncg.edu
Assistant Professor Microbiology
The Department of Biology at UNC Greensboro (UNCG) seeks an individual with a strong record of accomplishment in microbiology broadly defined for a tenure-track faculty position at the rank of Assista...
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Otto von Biz Markie @donachaidh.bsky.social · 11/09/2026
Lol my buddy just sent me another angle and it's somehow even more ridiculous
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Richard Lenski @relenski.bsky.social · 10/09/2026
A nice timeline of the #LTEE in the #MSU Spartan #Science magazine: spartanscience.natsci.msu.edu/evolution-in...
spartanscience.natsci.msu.edu
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Richard Lenski @relenski.bsky.social · 10/09/2026
Congratulations to Heran Darwin (@heran.bsky.social), Arturo Casadevall (acasadevall1.bsky.social), and all of the ASM awardees! asm.org/press-releas... @asm.org
asm.org
ASM Names 2027 Awards and Prize Program Honorees
ASM announces the recipients of its 2027 Awards and Prize Program. The awards recognize leading scientists and researchers in the microbial sciences for outstanding accomplishments and contributions.
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Sean Gibbons 🦠💩 @gibbological.bsky.social · 10/09/2026
Hello, NYU! engineering.nyu.edu/news/new-pro...
engineering.nyu.edu
New Professor Sean Gibbons Explores the Hidden World of the Human Microbiome | NYU Tandon School of Engineering
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Graham Coop @gcbias.bsky.social · 10/09/2026
I’m looking to hire an NIH funded postdoc to join our lab here at Davis (please RT). Ongoing areas of interest include: 1) polygenic signals of selection from time series, ARGs, GWAS, etc 2) The interpretation of GWAS, polygenic scores, & sources of confounding
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Grant @syncingsinking.bsky.social · 10/09/2026
This is just to say I have solved the open questions that were in your paper and which you were probably saving for your phd students Forgive me they were delicious so incentive-laden and followed so readily once your postdoc's drafts mysteriously found their way into my training data
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Julian Parkhill @julianparkhill.bsky.social · 08/09/2026
Chair in Bacteriology in Cambridge Department of Medicine. A great opportunity. Please circulate. www.cam.ac.uk/jobs/researc...
cam.ac.uk
Research Professor in the field of Bacteriology
Strengthening Cambridge's leadership in bacteriology research Bacterial infection and antimicrobial resistance remain among the most pressing global health challenges of our time. At Cambridge, the De...
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Drug Monkey @drugmonkey.bsky.social · 08/09/2026
And there it is. As rumored, and as predicted by YHN from the gitgo, enhanced triage of NIH grants will continue. grants.nih.gov/grants/guide...
grants.nih.gov
NOT-OD-26-114: Continuation of Modifications to Peer Review Practices
NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: Continuation of Modifications to Peer Review Practices NOT-OD-26-114. NIH
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Nick Stroustrup @nstroustrup.bsky.social · 05/09/2026
Did you know that the cells of old animals contain much less mRNA than the cells of young ones? Let me share with you some results from an ongoing project in the lab, where we are finding that a progressive depletion of total mRNA abundance is a crucial part of aging 1/22
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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 04/09/2026
New GWAS paradigm just dropped: in a meeting today @gcbias.bsky.social suggested that we eschew FDR and Bonferroni and instead draw a line on Manhattan plots at -log10(p)=11 as the Spinal Tap cutoff.
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Nature @nature.com · 04/09/2026
An agreement paves the way for hundreds of millions of dollars’ worth of projects to be transferred from the NIH’s institute for infectious diseases to the Department of Defense. go.nature.com/4ycEbk8
go.nature.com
Revealed: inside the US military's plan to tap huge sums from the NIH
An agreement paves the way for hundreds of millions of dollars’ worth of projects to be transferred from the NIH’s institute for infectious diseases to the Department of Defence.
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Moi Expósito-Alonso (MOILAB) @mexpositoalonso.bsky.social · 28/07/2026
The prestigious Miller Research Postdoctoral Fellowship is open! University of California, Berkeley This is a postdoc fellowship with substantial support and independence to be hosted at a lab at Berkeley, reach out with interests! miller.berkeley.edu/nominate-app...
miller.berkeley.edu
Miller Research Fellowship | Miller Institute for Basic Research in Science
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Ardem Patapoutian @ardemp.bskyverified.social · 31/08/2026
NIH's Aug 2026 proposal would scrap exact scores and percentiles for three broad bins (top = top 25%). With funding rates at 5% or lower, too much then rides on administrative discretion. It devalues peer review and is a deterrent to engage. Tell NIH before Oct 13. grants.nih.gov/grants/guide...
grants.nih.gov
NOT-OD-26-088: Request for Information (RFI) on Proposed Changes to Reporting Outcomes from NIH Peer Review
NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: Request for Information (RFI) on Proposed Changes to Reporting Outcomes from NIH Peer Review NOT-OD-26-088. NIH
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Eric Schares @eschares.bsky.social · 31/08/2026
🚨Update: Our analysis of global APC expenditure has now been expanded to cover more publishers (7 -> 14) and more years (2019-2025). We estimate $15B in APCs paid over seven years, $3.7B in 2025 alone. Elsevier crosses the $1B threshold by itself in 2025. arxiv.org/abs/2608.16322 #ScholComm
Line chart showing 5 biggest publishers from 2019-2025
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